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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Virtual Northern analysis of the human genome
Evan H Hurowitz1, Iddo Drori, Victoria C Stodden
1Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America.
Plos One
|May 24, 2007
Summary
Researchers measured human mRNA transcript lengths genome-wide, revealing extensive, unannotated transcript diversity and suggesting important regulatory roles for untranslated regions (UTRs) in eukaryotes.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Systematic measurement of human mRNA transcript lengths on a genome-wide scale was performed.
- The Virtual Northern technique was employed for this systematic analysis.
Purpose of the Study:
- To systematically measure human mRNA transcript lengths genome-wide.
- To identify novel transcript variants and assess transcript diversity.
- To investigate the relationship between mRNA length, untranslated regions (UTRs), and protein function.
Main Methods:
- Virtual Northern technique applied to human brain mRNA.
- Separation by gel electrophoresis followed by hybridization to cDNA microarrays.
- Comparison of measured transcript lengths with Refseq and H-Invitational full-length cDNA databases.
Main Results:
- 8,774 mRNA transcript lengths for at least 6,238 genes were measured with high confidence.
- Nearly half of the measurements potentially represent novel transcript variants.
- A linear relationship between ORF and mRNA lengths was observed, similar to yeast.
- Specific functional classes of proteins showed correlations with UTR lengths, conserved between human and yeast.
Conclusions:
- Human transcript diversity is extensive and largely unannotated.
- The generated length dataset can aid in judging cDNA completeness and annotating mRNA sequences.
- Conserved relationships between UTR lengths and protein function across species suggest a significant regulatory role for UTRs in eukaryotes.
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